NM_000441.2(SLC26A4):c.412_415+17del AND not provided

Clinical significance:Pathogenic (Last evaluated: Aug 3, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001381940.1

Allele description [Variation Report for NM_000441.2(SLC26A4):c.412_415+17del]

NM_000441.2(SLC26A4):c.412_415+17del

Gene:
SLC26A4:solute carrier family 26 member 4 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
7q22.3
Genomic location:
Preferred name:
NM_000441.2(SLC26A4):c.412_415+17del
HGVS:
  • NC_000007.14:g.107672245_107672265del
  • NG_008489.1:g.16611_16631del
  • NM_000441.2:c.412_415+17delMANE SELECT
  • NC_000007.13:g.107312690_107312710del
Molecular consequence:
  • NM_000441.2:c.412_415+17del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001580517Invitaecriteria provided, single submitter
Pathogenic
(Aug 3, 2020)
germlineclinical testing

PubMed (8)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Life-threatening metabolic alkalosis in Pendred syndrome.

Kandasamy N, Fugazzola L, Evans M, Chatterjee K, Karet F.

Eur J Endocrinol. 2011 Jul;165(1):167-70. doi: 10.1530/EJE-11-0101. Epub 2011 May 6.

PubMed [citation]
PMID:
21551164
PMCID:
PMC3118492

Two frequent missense mutations in Pendred syndrome.

Van Hauwe P, Everett LA, Coucke P, Scott DA, Kraft ML, Ris-Stalpers C, Bolder C, Otten B, de Vijlder JJ, Dietrich NL, Ramesh A, Srisailapathy SC, Parving A, Cremers CW, Willems PJ, Smith RJ, Green ED, Van Camp G.

Hum Mol Genet. 1998 Jul;7(7):1099-104.

PubMed [citation]
PMID:
9618166
See all PubMed Citations (8)

Details of each submission

From Invitae, SCV001580517.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (8)

Description

This variant results in the deletion of part of exon 4 (c.412_415+21delinsTGACA) of the SLC26A4 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with SLC26A4-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. This variant disrupts the p.Val138 amino acid residue in SLC26A4. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 21551164, 9618166, 11932316). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Loss-of-function variants in SLC26A4 are known to be pathogenic (PMID: 16283880, 25394566, 26252218, 26445815). For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 14, 2021

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